Starting phenix.real_space_refine on Thu Mar 5 21:53:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fce_31525/03_2026/7fce_31525.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fce_31525/03_2026/7fce_31525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fce_31525/03_2026/7fce_31525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fce_31525/03_2026/7fce_31525.map" model { file = "/net/cci-nas-00/data/ceres_data/7fce_31525/03_2026/7fce_31525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fce_31525/03_2026/7fce_31525.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16239 2.51 5 N 4157 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25542 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1043, 8142 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 51, 'TRANS': 991} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1043, 8142 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 51, 'TRANS': 991} Chain breaks: 8 bond proxies already assigned to first conformer: 8305 Chain: "B" Number of atoms: 8146 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 bond proxies already assigned to first conformer: 8293 Chain: "C" Number of atoms: 8146 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 bond proxies already assigned to first conformer: 8293 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 10.86, per 1000 atoms: 0.43 Number of scatterers: 25542 At special positions: 0 Unit cell: (135.042, 136.14, 162.489, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5032 8.00 N 4157 7.00 C 16239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 61 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 61 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 25.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.704A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.752A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.190A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 372 removed outlier: 4.094A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.750A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.136A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.418A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.322A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.645A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.418A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.644A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.333A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1037 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7816 1.34 - 1.47: 6740 1.47 - 1.59: 11403 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 26097 Sorted by residual: bond pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" C LYS A 462 " pdb=" N PRO A 463 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" N ARG B 457 " pdb=" CA ARG B 457 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.84e+00 bond pdb=" N SER A 494 " pdb=" CA SER A 494 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.52e+00 bond pdb=" N ILE A 472 " pdb=" CA ILE A 472 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.09e+00 ... (remaining 26092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 34165 2.35 - 4.70: 1252 4.70 - 7.04: 82 7.04 - 9.39: 10 9.39 - 11.74: 6 Bond angle restraints: 35515 Sorted by residual: angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 110.80 119.17 -8.37 2.13e+00 2.20e-01 1.55e+01 angle pdb=" N LEU A 455 " pdb=" CA LEU A 455 " pdb=" C LEU A 455 " ideal model delta sigma weight residual 113.50 108.67 4.83 1.23e+00 6.61e-01 1.54e+01 angle pdb=" C TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " ideal model delta sigma weight residual 109.75 103.39 6.36 1.65e+00 3.67e-01 1.49e+01 ... (remaining 35510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15381 17.58 - 35.16: 896 35.16 - 52.74: 178 52.74 - 70.32: 95 70.32 - 87.90: 28 Dihedral angle restraints: 16578 sinusoidal: 7466 harmonic: 9112 Sorted by residual: dihedral pdb=" CA LEU B 368 " pdb=" C LEU B 368 " pdb=" N TYR B 369 " pdb=" CA TYR B 369 " ideal model delta harmonic sigma weight residual -180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER C 371 " pdb=" C SER C 371 " pdb=" N THR C 372 " pdb=" CA THR C 372 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER A 371 " pdb=" C SER A 371 " pdb=" N THR A 372 " pdb=" CA THR A 372 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 16575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3265 0.079 - 0.159: 955 0.159 - 0.238: 46 0.238 - 0.318: 2 0.318 - 0.397: 2 Chirality restraints: 4270 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 370 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR A 495 " pdb=" N TYR A 495 " pdb=" C TYR A 495 " pdb=" CB TYR A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 370 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4267 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1307 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.504 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.330 2.00e-02 2.50e+03 2.82e-01 9.91e+02 pdb=" C7 NAG A1307 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.135 2.00e-02 2.50e+03 1.11e-01 1.53e+02 pdb=" C7 NAG C1307 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.023 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8440 2.85 - 3.37: 20721 3.37 - 3.88: 40988 3.88 - 4.39: 47432 4.39 - 4.90: 82022 Nonbonded interactions: 199603 Sorted by model distance: nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1BARG A1019 " model vdw 2.343 3.120 nonbonded pdb=" OD1 ASN C 777 " pdb=" NH1BARG C1019 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 777 " pdb=" NH1BARG B1019 " model vdw 2.345 3.120 nonbonded pdb=" O SER B 477 " pdb=" OG1 THR B 478 " model vdw 2.346 3.040 nonbonded pdb=" O SER A 477 " pdb=" OG1 THR A 478 " model vdw 2.347 3.040 ... (remaining 199598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 70 or resid 81 through 245 or resid 262 through \ 822 or resid 824 through 1018 or resid 1020 through 1308)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1308)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.800 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 26220 Z= 0.439 Angle : 1.003 11.739 35839 Z= 0.548 Chirality : 0.065 0.397 4270 Planarity : 0.008 0.288 4491 Dihedral : 12.930 87.899 10579 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 0.99 % Allowed : 3.47 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3077 helix: 0.89 (0.20), residues: 711 sheet: 0.63 (0.20), residues: 664 loop : -1.79 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.024 0.004 TYR C 265 PHE 0.022 0.004 PHE A 592 TRP 0.017 0.004 TRP B 886 HIS 0.008 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.01013 (26097) covalent geometry : angle 0.97828 (35515) SS BOND : bond 0.01175 ( 45) SS BOND : angle 2.27823 ( 90) hydrogen bonds : bond 0.14391 ( 1037) hydrogen bonds : angle 6.37837 ( 2796) link_BETA1-4 : bond 0.00498 ( 27) link_BETA1-4 : angle 1.55286 ( 81) link_NAG-ASN : bond 0.00575 ( 51) link_NAG-ASN : angle 3.02835 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 577 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.6157 (m-10) cc_final: 0.5529 (m-10) REVERT: B 844 ILE cc_start: 0.6885 (mt) cc_final: 0.6506 (mt) REVERT: C 14 GLN cc_start: 0.5295 (OUTLIER) cc_final: 0.4344 (mm-40) REVERT: C 751 ASN cc_start: 0.7140 (m110) cc_final: 0.6936 (m-40) REVERT: C 912 THR cc_start: 0.6991 (p) cc_final: 0.6786 (p) outliers start: 27 outliers final: 2 residues processed: 598 average time/residue: 0.1703 time to fit residues: 162.2368 Evaluate side-chains 292 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 207 HIS A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 501 ASN A 563 GLN A 580 GLN A 641 ASN A 703 ASN A 751 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1023 ASN A1036 GLN A1054 GLN A1064 HIS A1083 HIS A1101 HIS B 87 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 245 HIS B 394 ASN B 540 ASN B 563 GLN B 580 GLN B 641 ASN B 658 ASN B 703 ASN B 751 ASN B 925 ASN B1023 ASN B1036 GLN B1054 GLN B1064 HIS C 66 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 188 ASN C 218 GLN C 271 GLN C 394 ASN C 474 GLN C 540 ASN C 563 GLN C 580 GLN C 607 GLN C 658 ASN C 703 ASN C 751 ASN C 925 ASN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137157 restraints weight = 60370.463| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.55 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 26220 Z= 0.179 Angle : 0.708 17.158 35839 Z= 0.356 Chirality : 0.049 0.477 4270 Planarity : 0.004 0.051 4491 Dihedral : 7.557 59.451 5001 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 1.24 % Allowed : 9.11 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3077 helix: 1.25 (0.20), residues: 711 sheet: 0.62 (0.19), residues: 672 loop : -1.64 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1091 TYR 0.019 0.001 TYR C 756 PHE 0.038 0.002 PHE C 59 TRP 0.014 0.002 TRP B 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00399 (26097) covalent geometry : angle 0.66513 (35515) SS BOND : bond 0.00525 ( 45) SS BOND : angle 2.63743 ( 90) hydrogen bonds : bond 0.05659 ( 1037) hydrogen bonds : angle 5.47479 ( 2796) link_BETA1-4 : bond 0.00586 ( 27) link_BETA1-4 : angle 1.39558 ( 81) link_NAG-ASN : bond 0.01182 ( 51) link_NAG-ASN : angle 3.10763 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ARG cc_start: 0.6355 (mmm-85) cc_final: 0.6060 (mmt-90) REVERT: A 904 TYR cc_start: 0.6557 (m-10) cc_final: 0.5988 (m-10) REVERT: B 190 ARG cc_start: 0.6265 (mtt-85) cc_final: 0.5852 (mtp180) REVERT: B 207 HIS cc_start: 0.5474 (m-70) cc_final: 0.5134 (t70) REVERT: B 221 SER cc_start: 0.6336 (t) cc_final: 0.5995 (p) REVERT: B 233 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (pp) REVERT: B 787 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8285 (mm-40) REVERT: B 844 ILE cc_start: 0.6857 (mt) cc_final: 0.6571 (mt) REVERT: C 14 GLN cc_start: 0.4789 (OUTLIER) cc_final: 0.3099 (tp40) REVERT: C 740 MET cc_start: 0.8267 (tpp) cc_final: 0.8061 (ttm) outliers start: 34 outliers final: 19 residues processed: 344 average time/residue: 0.1663 time to fit residues: 92.6976 Evaluate side-chains 283 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 118 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1011 GLN B 137 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 137 ASN C1054 GLN C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115362 restraints weight = 67631.867| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.48 r_work: 0.3024 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 26220 Z= 0.172 Angle : 0.645 17.597 35839 Z= 0.329 Chirality : 0.047 0.300 4270 Planarity : 0.004 0.044 4491 Dihedral : 6.646 59.899 4999 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 1.28 % Allowed : 10.50 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3077 helix: 1.63 (0.20), residues: 693 sheet: 0.74 (0.20), residues: 628 loop : -1.43 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 577 TYR 0.018 0.001 TYR A 495 PHE 0.027 0.002 PHE B 643 TRP 0.018 0.001 TRP C1102 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00383 (26097) covalent geometry : angle 0.61803 (35515) SS BOND : bond 0.00719 ( 45) SS BOND : angle 2.25712 ( 90) hydrogen bonds : bond 0.04640 ( 1037) hydrogen bonds : angle 5.21125 ( 2796) link_BETA1-4 : bond 0.00573 ( 27) link_BETA1-4 : angle 1.36994 ( 81) link_NAG-ASN : bond 0.00438 ( 51) link_NAG-ASN : angle 2.19875 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6854 (mtt-85) cc_final: 0.6401 (mtm180) REVERT: A 428 ASP cc_start: 0.8373 (p0) cc_final: 0.7917 (p0) REVERT: A 470 THR cc_start: 0.8962 (p) cc_final: 0.8737 (p) REVERT: A 675 GLN cc_start: 0.6048 (pp30) cc_final: 0.5621 (pp30) REVERT: B 164 ASN cc_start: 0.5864 (t0) cc_final: 0.5621 (t0) REVERT: B 190 ARG cc_start: 0.6874 (mtt-85) cc_final: 0.5888 (mtp180) REVERT: B 207 HIS cc_start: 0.5826 (m-70) cc_final: 0.5257 (t70) REVERT: B 470 THR cc_start: 0.8212 (p) cc_final: 0.7883 (p) REVERT: B 503 VAL cc_start: 0.9219 (p) cc_final: 0.8957 (t) REVERT: B 821 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8434 (mt) REVERT: B 844 ILE cc_start: 0.6214 (mt) cc_final: 0.5923 (mt) REVERT: C 108 THR cc_start: 0.8348 (m) cc_final: 0.8100 (p) REVERT: C 319 ARG cc_start: 0.8189 (mtp85) cc_final: 0.6396 (mtt90) REVERT: C 643 PHE cc_start: 0.7621 (t80) cc_final: 0.7272 (t80) outliers start: 35 outliers final: 23 residues processed: 301 average time/residue: 0.1687 time to fit residues: 81.5996 Evaluate side-chains 259 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 265 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 66 HIS B 137 ASN B 164 ASN C 137 ASN C 271 GLN C 474 GLN C 641 ASN C1083 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107985 restraints weight = 60143.388| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.78 r_work: 0.2928 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 26220 Z= 0.136 Angle : 0.602 15.891 35839 Z= 0.302 Chirality : 0.046 0.316 4270 Planarity : 0.004 0.055 4491 Dihedral : 6.250 57.778 4994 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 1.13 % Allowed : 11.12 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3077 helix: 1.75 (0.20), residues: 705 sheet: 0.75 (0.20), residues: 618 loop : -1.27 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.016 0.001 TYR C1067 PHE 0.031 0.002 PHE B 643 TRP 0.012 0.001 TRP A1102 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00323 (26097) covalent geometry : angle 0.57800 (35515) SS BOND : bond 0.00537 ( 45) SS BOND : angle 2.19487 ( 90) hydrogen bonds : bond 0.04110 ( 1037) hydrogen bonds : angle 5.08077 ( 2796) link_BETA1-4 : bond 0.00502 ( 27) link_BETA1-4 : angle 1.39137 ( 81) link_NAG-ASN : bond 0.00321 ( 51) link_NAG-ASN : angle 1.88973 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7333 (mtt-85) cc_final: 0.6535 (mtm180) REVERT: A 299 THR cc_start: 0.8552 (p) cc_final: 0.8247 (t) REVERT: A 309 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 428 ASP cc_start: 0.8600 (p0) cc_final: 0.8109 (p0) REVERT: A 470 THR cc_start: 0.8971 (p) cc_final: 0.8757 (p) REVERT: B 190 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6276 (mtt180) REVERT: B 207 HIS cc_start: 0.6053 (m-70) cc_final: 0.5372 (t70) REVERT: B 503 VAL cc_start: 0.9273 (p) cc_final: 0.9073 (t) REVERT: B 606 ASN cc_start: 0.8104 (m-40) cc_final: 0.7602 (t0) REVERT: B 646 ARG cc_start: 0.7559 (mtm180) cc_final: 0.7047 (mtm180) REVERT: B 844 ILE cc_start: 0.6144 (mt) cc_final: 0.5938 (mt) REVERT: B 936 ASP cc_start: 0.7683 (m-30) cc_final: 0.7472 (m-30) REVERT: B 1118 ASP cc_start: 0.7926 (t0) cc_final: 0.7659 (m-30) REVERT: C 503 VAL cc_start: 0.9389 (p) cc_final: 0.9114 (t) REVERT: C 1141 LEU cc_start: 0.6911 (mp) cc_final: 0.6509 (tp) outliers start: 31 outliers final: 21 residues processed: 269 average time/residue: 0.1621 time to fit residues: 70.8031 Evaluate side-chains 231 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 952 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 267 optimal weight: 0.9990 chunk 308 optimal weight: 0.2980 chunk 183 optimal weight: 0.4980 chunk 279 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 270 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1005 GLN B 137 ASN C 271 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107359 restraints weight = 57706.588| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.63 r_work: 0.2922 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26220 Z= 0.113 Angle : 0.564 14.939 35839 Z= 0.284 Chirality : 0.045 0.317 4270 Planarity : 0.004 0.046 4491 Dihedral : 6.089 59.230 4994 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 1.06 % Allowed : 11.59 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3077 helix: 1.91 (0.20), residues: 704 sheet: 0.68 (0.20), residues: 630 loop : -1.15 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.015 0.001 TYR C1067 PHE 0.030 0.001 PHE B 643 TRP 0.012 0.001 TRP C1102 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00260 (26097) covalent geometry : angle 0.54598 (35515) SS BOND : bond 0.00562 ( 45) SS BOND : angle 1.64658 ( 90) hydrogen bonds : bond 0.03914 ( 1037) hydrogen bonds : angle 4.99348 ( 2796) link_BETA1-4 : bond 0.00481 ( 27) link_BETA1-4 : angle 1.27130 ( 81) link_NAG-ASN : bond 0.00308 ( 51) link_NAG-ASN : angle 1.72154 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7270 (m) REVERT: A 190 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.6598 (mtm180) REVERT: A 309 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 428 ASP cc_start: 0.8664 (p0) cc_final: 0.8163 (p0) REVERT: A 1092 GLU cc_start: 0.8503 (tp30) cc_final: 0.8185 (tt0) REVERT: B 47 VAL cc_start: 0.8176 (t) cc_final: 0.7816 (m) REVERT: B 190 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.5915 (mtm180) REVERT: B 207 HIS cc_start: 0.6181 (m-70) cc_final: 0.5646 (t70) REVERT: B 606 ASN cc_start: 0.8095 (m-40) cc_final: 0.7617 (t0) REVERT: B 646 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7049 (mtm180) REVERT: B 821 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8519 (mp) REVERT: B 844 ILE cc_start: 0.6175 (mt) cc_final: 0.5902 (mt) REVERT: C 14 GLN cc_start: 0.4996 (OUTLIER) cc_final: 0.4068 (mm-40) REVERT: C 503 VAL cc_start: 0.9417 (p) cc_final: 0.9163 (t) REVERT: C 690 GLN cc_start: 0.6203 (mm110) cc_final: 0.5761 (mm-40) REVERT: C 1141 LEU cc_start: 0.6804 (mp) cc_final: 0.6397 (tp) outliers start: 29 outliers final: 19 residues processed: 248 average time/residue: 0.1559 time to fit residues: 64.7488 Evaluate side-chains 224 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 72 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 422 ASN A 901 GLN A1005 GLN B 137 ASN C 137 ASN C 271 GLN C 394 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097287 restraints weight = 65295.678| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.27 r_work: 0.2745 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 26220 Z= 0.166 Angle : 0.627 16.124 35839 Z= 0.317 Chirality : 0.047 0.310 4270 Planarity : 0.004 0.044 4491 Dihedral : 6.374 59.977 4994 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.10 % Allowed : 12.11 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.31 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3077 helix: 1.68 (0.20), residues: 700 sheet: 0.67 (0.20), residues: 625 loop : -1.22 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 102 TYR 0.023 0.002 TYR C 265 PHE 0.031 0.002 PHE B 643 TRP 0.012 0.001 TRP C1102 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00404 (26097) covalent geometry : angle 0.60570 (35515) SS BOND : bond 0.00514 ( 45) SS BOND : angle 1.99625 ( 90) hydrogen bonds : bond 0.04784 ( 1037) hydrogen bonds : angle 5.21246 ( 2796) link_BETA1-4 : bond 0.00471 ( 27) link_BETA1-4 : angle 1.31996 ( 81) link_NAG-ASN : bond 0.00312 ( 51) link_NAG-ASN : angle 1.88950 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7380 (m) REVERT: A 190 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.6999 (mtm180) REVERT: A 309 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8238 (mm-30) REVERT: A 319 ARG cc_start: 0.7188 (mtt-85) cc_final: 0.6857 (mtt90) REVERT: A 422 ASN cc_start: 0.9466 (OUTLIER) cc_final: 0.9202 (m110) REVERT: A 489 TYR cc_start: 0.8740 (m-80) cc_final: 0.8499 (m-80) REVERT: A 1092 GLU cc_start: 0.8602 (tp30) cc_final: 0.8267 (tt0) REVERT: B 190 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.6740 (mtt-85) REVERT: B 207 HIS cc_start: 0.6567 (m-70) cc_final: 0.5888 (t-170) REVERT: B 606 ASN cc_start: 0.8383 (m-40) cc_final: 0.7754 (t0) REVERT: B 646 ARG cc_start: 0.7532 (mtm180) cc_final: 0.7049 (mtm180) REVERT: B 821 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 844 ILE cc_start: 0.6153 (mt) cc_final: 0.5925 (mt) REVERT: C 690 GLN cc_start: 0.6386 (mm110) cc_final: 0.5869 (mm-40) REVERT: C 1141 LEU cc_start: 0.6974 (mp) cc_final: 0.6641 (tp) outliers start: 30 outliers final: 22 residues processed: 237 average time/residue: 0.1808 time to fit residues: 67.9146 Evaluate side-chains 217 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 147 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 242 optimal weight: 0.0980 chunk 230 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 297 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 422 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN C 137 ASN C 271 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101695 restraints weight = 66210.744| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.18 r_work: 0.2852 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 26220 Z= 0.108 Angle : 0.557 15.085 35839 Z= 0.281 Chirality : 0.045 0.263 4270 Planarity : 0.004 0.043 4491 Dihedral : 6.145 59.506 4994 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 0.88 % Allowed : 12.58 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3077 helix: 1.78 (0.20), residues: 716 sheet: 0.74 (0.20), residues: 627 loop : -1.13 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.016 0.001 TYR C1067 PHE 0.029 0.001 PHE B 643 TRP 0.013 0.001 TRP C1102 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00246 (26097) covalent geometry : angle 0.53818 (35515) SS BOND : bond 0.00586 ( 45) SS BOND : angle 1.65400 ( 90) hydrogen bonds : bond 0.03990 ( 1037) hydrogen bonds : angle 5.05017 ( 2796) link_BETA1-4 : bond 0.00434 ( 27) link_BETA1-4 : angle 1.22723 ( 81) link_NAG-ASN : bond 0.00251 ( 51) link_NAG-ASN : angle 1.72079 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7223 (m) REVERT: A 309 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 489 TYR cc_start: 0.8714 (m-80) cc_final: 0.8491 (m-80) REVERT: A 936 ASP cc_start: 0.7790 (t70) cc_final: 0.7509 (m-30) REVERT: A 1136 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 47 VAL cc_start: 0.8535 (t) cc_final: 0.8115 (m) REVERT: B 190 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.6766 (mtt-85) REVERT: B 606 ASN cc_start: 0.8366 (m-40) cc_final: 0.7778 (t0) REVERT: B 646 ARG cc_start: 0.7414 (mtm180) cc_final: 0.6971 (mtm180) REVERT: B 821 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 844 ILE cc_start: 0.6215 (mt) cc_final: 0.5979 (mt) REVERT: C 14 GLN cc_start: 0.4867 (OUTLIER) cc_final: 0.4570 (mm-40) REVERT: C 102 ARG cc_start: 0.7168 (mmp-170) cc_final: 0.6935 (mmp-170) REVERT: C 137 ASN cc_start: 0.6827 (OUTLIER) cc_final: 0.6552 (m110) REVERT: C 489 TYR cc_start: 0.8817 (m-80) cc_final: 0.8473 (m-80) REVERT: C 690 GLN cc_start: 0.6341 (mm110) cc_final: 0.5832 (mm-40) REVERT: C 1141 LEU cc_start: 0.6850 (mp) cc_final: 0.6608 (tp) outliers start: 24 outliers final: 16 residues processed: 217 average time/residue: 0.1714 time to fit residues: 59.9347 Evaluate side-chains 202 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 146 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 422 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 271 GLN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101462 restraints weight = 56519.530| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 5.19 r_work: 0.2678 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26220 Z= 0.151 Angle : 0.597 15.824 35839 Z= 0.302 Chirality : 0.046 0.313 4270 Planarity : 0.004 0.042 4491 Dihedral : 6.253 59.671 4994 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 1.06 % Allowed : 12.73 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3077 helix: 1.72 (0.20), residues: 700 sheet: 0.72 (0.20), residues: 637 loop : -1.13 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.023 0.002 TYR C 756 PHE 0.026 0.002 PHE B 643 TRP 0.011 0.001 TRP C1102 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00368 (26097) covalent geometry : angle 0.57842 (35515) SS BOND : bond 0.00509 ( 45) SS BOND : angle 1.77453 ( 90) hydrogen bonds : bond 0.04487 ( 1037) hydrogen bonds : angle 5.09184 ( 2796) link_BETA1-4 : bond 0.00432 ( 27) link_BETA1-4 : angle 1.28772 ( 81) link_NAG-ASN : bond 0.00237 ( 51) link_NAG-ASN : angle 1.79649 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 828 LEU cc_start: 0.8640 (mm) cc_final: 0.8379 (mt) REVERT: A 936 ASP cc_start: 0.7781 (t70) cc_final: 0.7535 (m-30) REVERT: B 47 VAL cc_start: 0.8455 (t) cc_final: 0.8071 (m) REVERT: B 190 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.6791 (mtt-85) REVERT: B 606 ASN cc_start: 0.8543 (m-40) cc_final: 0.7855 (t0) REVERT: B 607 GLN cc_start: 0.8137 (tt0) cc_final: 0.7796 (mt0) REVERT: B 821 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8565 (mp) REVERT: B 844 ILE cc_start: 0.6070 (mt) cc_final: 0.5846 (mt) REVERT: B 1111 GLU cc_start: 0.9098 (tt0) cc_final: 0.8889 (tt0) REVERT: C 14 GLN cc_start: 0.4809 (OUTLIER) cc_final: 0.4545 (mm-40) REVERT: C 690 GLN cc_start: 0.6360 (mm110) cc_final: 0.5861 (mm-40) REVERT: C 1141 LEU cc_start: 0.6884 (mp) cc_final: 0.6624 (tp) outliers start: 29 outliers final: 20 residues processed: 210 average time/residue: 0.1719 time to fit residues: 58.1960 Evaluate side-chains 201 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 952 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 84 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 139 optimal weight: 0.0270 chunk 278 optimal weight: 2.9990 chunk 128 optimal weight: 0.0020 chunk 261 optimal weight: 7.9990 overall best weight: 1.1650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 481 ASN C 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099123 restraints weight = 63056.034| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.90 r_work: 0.2748 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26220 Z= 0.134 Angle : 0.586 15.548 35839 Z= 0.295 Chirality : 0.045 0.272 4270 Planarity : 0.004 0.043 4491 Dihedral : 6.209 58.129 4994 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.88 % Allowed : 12.95 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3077 helix: 1.72 (0.20), residues: 712 sheet: 0.67 (0.20), residues: 651 loop : -1.13 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.019 0.001 TYR C 756 PHE 0.018 0.001 PHE C 817 TRP 0.011 0.001 TRP C1102 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00321 (26097) covalent geometry : angle 0.56486 (35515) SS BOND : bond 0.00616 ( 45) SS BOND : angle 2.09043 ( 90) hydrogen bonds : bond 0.04231 ( 1037) hydrogen bonds : angle 5.06611 ( 2796) link_BETA1-4 : bond 0.00403 ( 27) link_BETA1-4 : angle 1.23561 ( 81) link_NAG-ASN : bond 0.00221 ( 51) link_NAG-ASN : angle 1.75973 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6617 (mtt180) cc_final: 0.6098 (mtt180) REVERT: A 828 LEU cc_start: 0.8625 (mm) cc_final: 0.8412 (mt) REVERT: B 47 VAL cc_start: 0.8495 (t) cc_final: 0.8091 (m) REVERT: B 190 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.6614 (mtt180) REVERT: B 529 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7004 (tptp) REVERT: B 606 ASN cc_start: 0.8486 (m-40) cc_final: 0.7838 (t0) REVERT: B 607 GLN cc_start: 0.8057 (tt0) cc_final: 0.7770 (mt0) REVERT: B 821 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8564 (mp) REVERT: B 844 ILE cc_start: 0.6104 (mt) cc_final: 0.5876 (mt) REVERT: C 64 TRP cc_start: 0.7167 (t60) cc_final: 0.6757 (t60) REVERT: C 489 TYR cc_start: 0.8786 (m-80) cc_final: 0.8414 (m-80) REVERT: C 613 GLN cc_start: 0.8131 (tt0) cc_final: 0.7804 (tt0) REVERT: C 690 GLN cc_start: 0.6300 (mm110) cc_final: 0.5785 (mm-40) REVERT: C 1141 LEU cc_start: 0.6841 (mp) cc_final: 0.6630 (tp) outliers start: 24 outliers final: 20 residues processed: 205 average time/residue: 0.1724 time to fit residues: 57.1133 Evaluate side-chains 202 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 265 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 394 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN B 164 ASN B 481 ASN C 271 GLN C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105054 restraints weight = 52443.695| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.64 r_work: 0.2728 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 26220 Z= 0.110 Angle : 0.556 14.982 35839 Z= 0.279 Chirality : 0.044 0.280 4270 Planarity : 0.004 0.045 4491 Dihedral : 6.039 59.721 4994 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.77 % Allowed : 13.02 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3077 helix: 1.91 (0.20), residues: 712 sheet: 0.69 (0.20), residues: 659 loop : -1.02 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.015 0.001 TYR C1067 PHE 0.019 0.001 PHE C 643 TRP 0.012 0.001 TRP C1102 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00257 (26097) covalent geometry : angle 0.53729 (35515) SS BOND : bond 0.00450 ( 45) SS BOND : angle 1.80746 ( 90) hydrogen bonds : bond 0.03828 ( 1037) hydrogen bonds : angle 4.96429 ( 2796) link_BETA1-4 : bond 0.00406 ( 27) link_BETA1-4 : angle 1.16473 ( 81) link_NAG-ASN : bond 0.00215 ( 51) link_NAG-ASN : angle 1.65001 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6834 (mtt180) cc_final: 0.6534 (mtt90) REVERT: B 47 VAL cc_start: 0.8480 (t) cc_final: 0.8112 (m) REVERT: B 190 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.6558 (mtp85) REVERT: B 529 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7042 (tptp) REVERT: B 606 ASN cc_start: 0.8598 (m-40) cc_final: 0.7902 (t0) REVERT: B 646 ARG cc_start: 0.7396 (mtm180) cc_final: 0.6968 (mtm180) REVERT: B 844 ILE cc_start: 0.6121 (mt) cc_final: 0.5909 (mt) REVERT: B 902 MET cc_start: 0.9157 (tpt) cc_final: 0.8769 (tpt) REVERT: C 64 TRP cc_start: 0.7315 (t60) cc_final: 0.6861 (t60) REVERT: C 489 TYR cc_start: 0.8857 (m-80) cc_final: 0.8493 (m-80) REVERT: C 613 GLN cc_start: 0.8161 (tt0) cc_final: 0.7858 (tt0) REVERT: C 690 GLN cc_start: 0.6354 (mm110) cc_final: 0.5945 (mm-40) REVERT: C 1141 LEU cc_start: 0.6984 (mp) cc_final: 0.6731 (tt) outliers start: 21 outliers final: 19 residues processed: 210 average time/residue: 0.1746 time to fit residues: 59.1865 Evaluate side-chains 200 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 127 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 174 optimal weight: 0.0470 chunk 132 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN B1119 ASN C 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094434 restraints weight = 71964.940| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.17 r_work: 0.2818 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 26220 Z= 0.108 Angle : 0.555 14.919 35839 Z= 0.281 Chirality : 0.044 0.299 4270 Planarity : 0.004 0.050 4491 Dihedral : 5.987 57.649 4994 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.66 % Allowed : 13.28 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3077 helix: 1.96 (0.20), residues: 707 sheet: 0.72 (0.20), residues: 644 loop : -0.99 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 577 TYR 0.015 0.001 TYR C1067 PHE 0.016 0.001 PHE A 643 TRP 0.011 0.001 TRP C1102 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00249 (26097) covalent geometry : angle 0.53673 (35515) SS BOND : bond 0.00516 ( 45) SS BOND : angle 1.82564 ( 90) hydrogen bonds : bond 0.03792 ( 1037) hydrogen bonds : angle 4.93291 ( 2796) link_BETA1-4 : bond 0.00388 ( 27) link_BETA1-4 : angle 1.15759 ( 81) link_NAG-ASN : bond 0.00201 ( 51) link_NAG-ASN : angle 1.61448 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6279.55 seconds wall clock time: 108 minutes 23.68 seconds (6503.68 seconds total)